In this issue …

Environmental monitoring

Dissection of a pig's heart - learning more

Using spreadsheets in biological education

Children's understanding of eating     

Scuola ed educazione naturalistica

Abstract

School and naturalistic education. In order that mankind may correctly fit in the balance of nature young people must be given the right scientific preparation during school years. This is why a better training of science teachers would be so important especially in Italy, where they come straight from University having followed various types of scientific degree courses, mainly theoretical, and with no special preparation for teaching.

The main basic requirement for a science teacher is that he has a solid preparation for laboratory but especially for field work. All other kinds of scientific and pedagogic knowledge is of course important but not as indispensable. It is therefore necessary to give science teachers the naturalistic training that University syllabuses do not provide for. At the same time work done inside the school should be supported from the outside by other organizations such as the Field Studies Council in England, or the « keeper-guides » of Israeli natural parks. In the present Italian school system one immediate step could be taken: teachers of « scientific observations » should not confine themselves to lecturing in classrooms but should spend most of their allotted time with their classes in the field or in the laboratory, in the same way as for instance teachers of « technical applications » do their teaching only in the workshop.     

The effects of oestrogenic substances on two components of freshwater ecosystems

The effects of an oestrogenic compound, similar to those recently linked with falling human sperm counts, were investigated in two common freshwater organisms commonly used in education

Oestrogenic compounds have recently been linked with falling sperm counts in human males and also with cancer of the testes and breast. If these compounds can have such dangerous and dramatic effects in humans, as well as affecting sexual behaviour and physiology of fish, what effects do they have on other members of freshwater food chains? The aim of this investigation was to perform some simple experiments using basic laboratory facilities for student research projects. Daphnia, an important primary consumer and food source for fish, was exposed to increasing amounts of ethynyloestradiol, an oestrogen commonly used in contraceptive tablets. The higher concentrations of the oestrogen (0.1 to 1.0 ppm) were found to significantly reduce the heart rate of the Daphnia after approximately 30 minutes' exposure. It is proposed that such a reduction in the activity of oestrogen exposed Daphnia would make them more prone to predation and therefore increase the accumulation of oestrogens by fish. A further experiment investigated the effects of the oestrogen on photosynthesis in Elodea, a common pond weed. The same concentrations of ethynyloestradiol increased photosynthetic rates which could lead to a proliferation in growth. This again would promote the transfer of these compounds if they accumulate in the tissues for aquatic plants. These experiments on a currently significant topic were performed using readily available organisms and a small capital expenditure, thus making them a pertinent and interesting practical for both Alevel and undergraduate students.     

Ligand-based pharmacophore mapping and virtual screening for identification of potential discoidin domain receptor 1 inhibitors

Abbreviations ADME absorption, distribution, metabolism, and excretion

MMGB/SA molecular mechanics generalized born surface area

IFD induced fit docking

RTK receptor tyrosine kinase

NSCLC non-small-cell lung cancer

ATP adenosine triphosphate

OPLS optimized potential for liquid stimulation

RMSD root mean square deviation

HTVS high-throughput virtual screening

SP standard precision

XP extra precision

OPLS-AA optimized potential for liquid stimulation-all atom

MD molecular simulation

MME molecular mechanics energies

SGB surface generalized born

POPC membrane 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine membrane

PDB Protein Data Bank

DDR1 discoidin domain receptor 1

DDR2 discoidin domain receptor 2

DDRs discoidin domain receptors

ECM extracellular matrix

TIP4P transferable intermolecular potential 4 point

NPT constant particle number, pressure and temperature

RMSF root mean square fluctuation

Communicated by Ramaswamy H. Sarma     

Vorinostat,a possible alternative to metronidazole for the treatment of amebiasis caused by Entamoeba histolytica

Abbreviations SAHA suberoylanilide hydroxamic acid

EhHDAC Histone Deacetylase from Entamoeba histolytica

Rg Radius of gyration

RMSD root-mean-square deviation

RMSF root-mean-square fluctuation

MDS molecular dynamics simulation

VMD Visual Molecular Dynamics

NAMD Nanoscale Molecular Dynamics

PBC periodic boundary conditions

PME Particle Mesh Ewald

3D three-dimensional

Cα alpha carbon

FDA Food and Drug Administration

ns nanoseconds

GPU CUDA Graphics Processing Unit Compute Unified Device Architecture

Communicated by Ramaswamy H. Sarma     

Defining quality in visual art education for young children: Building on the position statement of the Early Childhood Art Educators

ABSTRACT

This article reflects the collective voices of four early childhood visual arts educators, each of whom is a member of the Early Childhood Art Educators (ECAE) Issues Group of the National Arts Educators Association. The authors frame the article around the ECAE position statement, Art: Essential for Early Learning (2016) Early Childhood Art Educators. (2016). Art: Essential for early learning, position statement on early childhood art education (Rev. ed.). Reston, VA: National Art Education Association. Retrieved from https://www.arteducators.org/advocacy/articles/127-position-statement-on-early-childhood-art-education [Google Scholar], which focuses on the central role of art interactions among young children, educators, environments, and materials. The authors describe eight principles that underlie the statement from philosophical viewpoints, and provide practical examples of the principles in action. Amid a varied policy landscape for visual art in early childhood, the authors assert that children need organized, materials-rich environments that invite discovery, interaction, sensory and kinesthetic exploration, wonder, inquiry, and imagination in relationship with responsive educators who value young children's diverse abilities, interests, questions, ideas, and cultural experiences. The authors explore issues and possibilities resulting when educators work to bring visual arts fully and dynamically into the lives of young children in diverse education and care spaces. In closing, the authors explore the realities of visual arts policies in the early childhood education and art education fields while emphasizing the critical need for supportive pedagogical practices in all early childhood classrooms.     

Evolutionary significance and functional characterization of streptomycin adenylyltransferase from Serratia marcescens

Abstract

Complete functional annotations of proteins are essential to understand the role and mechanisms in pathogenesis. Aminoglycoside nucleotidyltransferases are the subclasses of aminoglycosides modifying enzymes conferring resistance to organisms. Insight into the structural and functional understanding of nucleotidyltransferase family protein provides vital information to combat pathogenesis. Phylogenetic analysis is employed to identify the evolutionary significance and common motif’s present among the homologs of nucleotidyltransferase family protein. Structure, sequence based approaches and molecular docking were implemented to predict the exact function of the protein. Wide distribution of the nucleotidyltransferase family protein in gram-positive and gram-negative organisms are evidenced from phylogenetic analysis. Five common motifs were present in all the homolog’s of nucleotidyltransferase family protein. Sequence-structure based functional annotations predicts that the targeted protein function as ATP-Mg dependent streptomycin adenylyltransferase. Structural comparisons and docking studies correlate well with the identified function. The complete function of nucleotidyltransferase family protein was identified as Streptomycin adenylyltransferase and it could be targeted as a potential therapeutic target to overcome antibiotic resistance.

Communicated by Ramaswamy H. Sarma

Abbreviations AAC aminoglycoside acetyltransferases

AME aminoglycoside modifying enzyme

ANT aminoglycoside nucleotidyltransferases

APH aminoglycoside phosphotransferases

ATP adenosine triphosphate

CASTp computer atlas and surface topography of proteins

DUF domains of unknown function

Glide grid-based ligand docking with energetic

HMM hidden Markov model

MAST motif alignment and search tool

MEGA molecular evolutionary genetics analysis

MEME multiple Em for motif elicitation

MSA multiple sequence alignment

NMP nucleoside monophosphate

NTP nucleoside triphosphate

NT nucleotidyltransferase

OPLS optimized potential for liquid simulation

XP extra precision

     

Effect of tea catechins on tRNA structure and dynamics

Abbreviations C catechin

ECG epicatechin gallate

EGCG Epigallocatechin gallate

A Adenine

C cytosine

G Guanine

U uracil

FTIR Fourier transform infrared

Communicated by Ramaswamy H. Sarma     

Modulation of p53 N-terminal transactivation domain 2 conformation ensemble and kinetics by phosphorylation

Abstract

Phosphorylation of protein is critical for various cell processes, which preferentially happens in intrinsically disordered proteins (IDPs). How phosphorylation modulates structural ensemble of disordered peptide remains largely unexplored. Here, using replica exchange molecular dynamics (REMD) and Markov state model (MSM), the conformational distribution and kinetics of p53 N-terminal transactivation domain (TAD) 2 as well as its dual-site phosphorylated form (pSer46, pThr55) were simulated. It reveals that the dual phosphorylation does not change overall size and secondary structure element fraction, while a change in the distribution of hydrogen bonds induces slightly more pre-existing bound helical conformations. MSM analysis indicates that the dual phosphorylation accelerates conformation exchange between disordered and order-like states in target-binding region. It suggests that p53 TAD2 after phosphorylation would be more apt to bind to both the human p62 pleckstrin homology (PH) domain and the yeast tfb1?PH domain through different binding mechanism, where experimentally it exhibits an extended and α-helix conformation, respectively, with increased binding strength in both complexes. Our study implies except binding interface, both conformation ensemble and kinetics should be considered for the effects of phosphorylation on IDPs. Abbreviations IDPs intrinsically disordered proteins

REMD replica exchange molecular dynamics

MSM Markov state model

TAD transactivation domain

PH pleckstrin homology

PRR proline-rich region

DBD DNA-binding domain

TET Tetramerization domain

REG regulatory domain

MD molecular dynamics

PME particle-mesh Ewald

TICA time-lagged independent component analysis

CK Chapman–Kolmogorov

GMRQ generalized matrix Rayleigh quotient

SARW self-avoiding random walk

KID kinase-inducible domain

MFPT mean first passage time

DSSP definition of secondary structure of proteins

RMSD root mean square deviation

R_g radius of gyration

R_ee end to end distance

Communicated by Ramaswamy H. Sarma     

Rational MD simulations for improvement the affinity of nanobody against PlGF (placenta growth factor): mutagenesis based on electrostatic interactions

Abbreviations COM center of mass distance

MD molecular dynamics

MM-PBSA Molecular Mechanics Poisson–Boltzmann Surface Area

Nb nanobody

PlGF placenta growth factor

Rg radius of gyration

RMSD root mean-square deviation

SASA solvent-accessible surface area

VEGF vascular endothelial growth factor

     

Molecular dynamics simulation studies on influenza A virus H5N1 complexed with sialic acid and fluorinated sialic acid

Abbreviations HA Hemagglutinin

MD Molecular Dynamics

MM-PBSA Molecular Mechanics Poisson–Boltzmann Surface Area

NA Neuraminidase

NAMD Nanoscale Molecular Dynamic Simulation

PMEMD Particle Mesh Ewald Molecular Dynamics

RMSD Root-Mean-Square Deviation

RMSF Root-Mean-Square Fluctuation

SIA sialic acid

VMD Visual Molecular Dynamics

Communicated by Ramaswamy H. Sarma     

Soft regions of protein surface are potent for stable dimer formation

Abstract

By having knowledge about the characteristics of protein interaction interfaces, we will be able to manipulate protein complexes for therapies. Dimer state is considered as the primary alphabet of the most proteins’ quaternary structure. The properties of binding interface between subunits and of noninterface region define the specificity and stability of the intended protein complex. Considering some topological properties and amino acids’ affinity for binding in interfaces of protein dimers, we construct the interface-specific recurrence plots. The data obtained from recurrence quantitative analysis, and accessibility-related metrics help us to classify the protein dimers into four distinct classes. Some mechanical properties of binding interfaces are computed for each predefined class of the dimers. The computed mechanical characteristics of binding patch region are compared with those of nonbinding region of proteins. Our observations indicate that the mechanical properties of protein binding sites have a decisive impact on determining the dimer stability. We introduce a new concept in analyzing protein structure by considering mechanical properties of protein structure. We conclude that the interface region between subunits of stable dimers is usually mechanically softer than the interface of unstable protein dimers. Abbreviations AAB average affinity for binding

ANM anisotropic network model

APC affinity propagation clustering

ASA accessible surface area

CCD inter residues distance

CSC complex stability code

DM distance matrix

ΔG_diss PISA-computed dissociation free energy

GNM Gaussian normal mode analysis

NMA normal mode analysis

PBP protein binding patch

PISA proteins, interfaces, structures and assemblies

rASA relative accessible area in respect to unfolded state of residues

RM recurrence matrix

rP relative protrusion

RP recurrence plot

RQA recurrence quantitative analysis

SEM standard error of mean

Communicated by Ramaswamy H. Sarma     

Structural dynamics behind variants in pyrazinamidase and pyrazinamide resistance

Abstract

Pyrazinamide (PZA) is an important component of first-line anti-tuberculosis (anti-TB) drugs. The anti-TB agent is activated into an active form, pyrazinoic acid (POA), by Mycobacterium tuberculosis (MTB) pncA gene encoding pyrazinamidase (PZase). The major cause of PZA-resistance has been associated with mutations in the pncA gene. We have detected several novel mutations including V131F, Q141P, R154T, A170P, and V180F (GeneBank Accession No. MH461111) in the pncA gene of PZA-resistant isolates during PZA drug susceptibility testing followed by pncA gene sequencing. Here, we investigated molecular mechanism of PZA-resistance by comparing the results of experimental and molecular dynamics. The mutants (MTs) and wild type (WT) PZase structures in apo and complex with PZA were subjected to molecular dynamic simulations (MD) at the 40?ns. Multiple factors, including root mean square deviations (RMSD), binding pocket, total energy, dynamic cross correlation, and root mean square fluctuations (RMSF) of MTs and WT were compared. The MTs attained a high deviation and fluctuation compared to WT. Binding pocket volumes of the MTs, were found, lower than the WT, and the docking scores were high than WT while shape complementarity scores were lower than that of the WT. Residual motion in MTs are seemed to be dominant in anti-correlated motion. Mutations at locations, V131F, Q141P, R154T, A170P, and V180F, might be involved in the structural changes, possibly affecting the catalytic property of PZase to convert PZA into POA. Our study provides useful information that will enhance the understanding for better management of TB. Abbreviations DST drug susceptibility testing

Δelec electrostatic energy

LJ Lowenstein–Jensen medium

MGIT mycobacterium growth indicator tubes

MTs mutants

MD molecular dynamic simulations

MTB Mycobacterium tuberculosis

NALC–NaOH N-acetyl-l-cysteine–sodium hydroxide

NIH National Institutes of Health

NPT amount of substance (N), pressure (P) temperature (T)

NVT moles (N), volume (V) temperature (T)

PZase pyrazinamidase

Δps polar solvation energy

PTRL Provincial Tuberculosis Reference Laboratory

RMSD root mean square deviations

RMSF root mean square fluctuations

ΔSASA solvent accessible surface area energy

TB tuberculosis

GTotal total binding free energy

ΔvdW Van der Waals energy

WT wild type

Communicated by Ramaswamy H. Sarma     

Virtual identification of novel PPARα/γ dual agonists by 3D-QSAR,molecule docking and molecular dynamics studies

Abstract

Peroxisome proliferator-activated receptors (PPARs) are considered important targets for the treatment of Type 2 diabetes (T2DM). To accelerate the discovery of PPAR α/γ dual agonists, the comparative molecular field analysis (CoMFA) were performed for PPARα and PPARγ, respectively. Based on the molecular alignment, highly predictive CoMFA model for PPARα was obtained with a cross-validated q² value of 0.741 and a conventional r² of 0.975 in the non-cross-validated partial least-squares (PLS) analysis, while the CoMFA model for PPARγ with a better predictive ability was shown with q² and r² values of 0.557 and 0.996, respectively. Contour maps derived from the 3D-QSAR models provided information on main factors towards the activity. Then, we carried out structural optimization and designed several new compounds to improve the predicted biological activity. To investigate the binding modes of the predicted compounds in the active site of PPARα/γ, a molecular docking simulation was carried out. Molecular dynamic (MD) simulations indicated that the predicted ligands were stable in the active site of PPARα/γ. Therefore, combination of the CoMFA and structure-based drug design results could be used for further structural alteration and synthesis and development of novel and potent dual agonists. Abbreviations DM diabetes mellitus

T2DM type 2 diabetes

PPARs peroxisome proliferator-activated receptors

LBDD ligand based drug design

3D-QSAR three-dimensional quantitative structure activity relationship

CoMFA comparative molecular field analysis

PLS partial least square

LOO leave-one-out

q² cross-validated correlation coefficient

ONC optimal number of principal components

r² non-cross-validated correlation coefficient

SEE standard error of estimate

F the Fischer ratio

r²_pred predictive correlation coefficient

DBD DNA binding domain

MD molecular dynamics

RMSD root-mean-square deviation

RMSF root mean square fluctuations

Communicated by Ramaswamy H. Sarma     

The pathogenicity,structural and functional exploration of human HMGB1 single nucleotide polymorphisms using in silico study

Abstract

The human HMGB1 gene mutations have a major impact on several immune-related diseases and cancer. The detrimental effect of non-synonymous mutations of HMGB1 has not been investigated yet, hence the present study aims to examine single nucleotide polymorphisms and their implications on the structure-function of human HMGB1. The multifaceted HMGB1 protein acts as pleiotropic cytokine and regulates essential genes for coordinated cellular functions. The mutational effect on HMGB1 was analyzed by sequence-based homology methods, supervised learning methods, and structure-based methods. The study identified 58 non-synonymous mutations in human HMGB1, out of which only 2 mutations; R10T (rs61742222) and F103C (rs61733675) were classified as the SNPs with highest deleterious and disease-causing mutants. The effect of these mutations in structure of HMGB1 was scrutinized and the R10T mutant found to have a distinct structural behaviour in the B-box domain. In addition, R10T mutant predicted that it affects the MoRF function of HMGB1 and it could disrupt the DNA binding or/and protein partner interaction activity by HMGB1. F103C mutation takes place at the TLR binding and cytokine inducing region of HMGB1, hence it could affect the protein binding activity which involves in many cellular signaling. The study identified potent mutations R10T (a cancer-causing somatic mutation) and F103C (a novel mutation) and these mutations either directly or indirectly hinder DNA binding activity and TLR and cytokine binding of HMGB1. These findings will help in understanding the molecular basis of these promising mutations and functional role of human HMGB1 in cancer and immunological diseases.

Abbreviations AGER Advanced glycosylation end product-specific receptor

CXCL Chemokine (C-X-C motif) ligand

dbSNP The single nucleotide polymorphism database

HMGB1 High mobility group box 1

LINCS LINear Constraint Solver

MDS Molecular dynamics simulation

MoRF Molecular recognition features

NPT Number of particle, Pressure and Temperature

NVT Number of particle, Volume and Temperature

nsSNP Non-synonymous SNP

PBC Partial boundary condition

PCA Principal component analysis

PME Partial mesh Ewald

RMSD Root mean square deviation

RMSF Root mean square fluctuation

SNP Single nucleotide polymorphism

SPC Single-point charge

TLR Toll-like receptor

UTR Un-translated Region

Communicated by Ramaswamy H. Sarma     

Identifying potential GluN2B subunit containing N-Methyl-D-aspartate receptor inhibitors: an integrative in silico and molecular modeling approach

Abstract

N-methyl-D-aspartate receptors (NMDARs), a class of ligand-gated ion channels, are involved in non-selective cation transport across the membrane. These are contained in glutamatergic synapse and produce excitatory effects leading to synaptic plasticity and memory function. GluN1-GluN2B, a subtype of NMDAR(s), has significant role in neurodegeneration, amyloid β (Aβ) induced synaptic dysfunction and loss. Thus, targeting and inhibiting GluN1-GluN2B may be effective in the management of neurodegenerative diseases including Alzheimer’s disease. In the present study, ligand and structure-based approaches were tried to identify the inhibitors. The pharmacophore, developed from co-crystallised ifenprodil, afforded virtual hits, which were further subjected through drug likeliness and PAINS filters to remove interfering compounds. Further comprehensive docking studies, free energy calculations and ADMET studies resulted in two virtual leads. The leads, ZINC257261614 and ZINC95977857 displayed good docking scores of ?12.90 and ?12.20?Kcal/mol and free binding energies of ?60.83 and ?61.83?Kcal/mol, respectively. The compounds were having acceptable predicted ADMET profiles and were subjected to molecular dynamic (MD) studies. The MD simulation produced stable complexes of these ligands with GluN1-GluN2B subunit having protein and ligand RMSD in acceptable limit. Abbreviations AD Alzheimer's disease

ADME Absorption distribution metabolism and excretion

ATD Amino terminal domain

BBB Blood-brain barrier

CNS Central nervous system

CREB cAMP response element binding protein

CTD Carboxy-terminal domain

Glu Glutamate

GMQE Global model quality estimation

HTVS High throughput virtual screening

HIA Human intestinal absorption

LGA Lamarckian genetic algorithm

MD Molecular dynamics

MM-GBSA Molecular mechanics, the Generalised Born model for Solvent Accessibility

NMDAR N-methyl-D-aspartate receptors

PAINS Pan assay interference compounds

RMSD Root-mean square deviation

RMSF Root-mean-square fluctuation

SMARTS SMILES arbitrary target specification

SP standard precision

XP extra precision

Communicated by Ramaswamy H. Sarma     

Autophagy and inflammation in chronic respiratory disease

Persistent inflammation within the respiratory tract underlies the pathogenesis of numerous chronic pulmonary diseases including chronic obstructive pulmonary disease, asthma and pulmonary fibrosis. Chronic inflammation in the lung may arise from a combination of genetic susceptibility and environmental influences, including exposure to microbes, particles from the atmosphere, irritants, pollutants, allergens, and toxic molecules. To this end, an immediate, strong, and highly regulated inflammatory defense mechanism is needed for the successful maintenance of homeostasis within the respiratory system. Macroautophagy/autophagy plays an essential role in the inflammatory response of the lung to infection and stress. At baseline, autophagy may be critical for inhibiting spontaneous pulmonary inflammation and fundamental for the response of pulmonary leukocytes to infection; however, when not regulated, persistent or inefficient autophagy may be detrimental to lung epithelial cells, promoting lung injury. This perspective will discuss the role of autophagy in driving and regulating inflammatory responses of the lung in chronic lung diseases with a focus on potential avenues for therapeutic targeting.

Abbreviations AR allergic rhinitis

AM alveolar macrophage

ATG autophagy-related

CF cystic fibrosis

CFTR cystic fibrosis transmembrane conductance regulator

COPD chronic obstructive pulmonary disease

CS cigarette smoke

CSE cigarette smoke extract

DC dendritic cell

IH intermittent hypoxia

IPF idiopathic pulmonary fibrosis

ILD interstitial lung disease

MAP1LC3B microtubule associated protein 1 light chain 3 beta

MTB Mycobacterium tuberculosis

MTOR mechanistic target of rapamycin kinase

NET neutrophil extracellular traps

OSA obstructive sleep apnea

PAH pulmonary arterial hypertension

PH pulmonary hypertension

ROS reactive oxygen species

TGFB1 transforming growth factor beta 1

TNF tumor necrosis factor